Validation of gene variants potentially related to orofacial clefts in the polish population

Abstract Orofacial clefts (OFCs) are common congenital birth defects affecting the lip and palate, with an incidence of about 1 in 700 newborns globally. The severity of the cleft depends on the stage of fetal development at which the process was interrupted. These malformations impact essential functions leading to long-term health and social challenges. Approximately 50% of OFC cases occur as isolated, non-syndromic defects, influenced by genetic predispositions and environmental factors. This case–control study investigated associations between four SNPs—rs227731 ( NOG ), rs2166975 ( TGFA ), rs142167 ( NSF ), and rs2205181 ( TGFB3 )—and non-syndromic orofacial clefts in a Polish cohort comprising 209 cases and 418 controls. Cases were recruited from two orthodontic centers, and control DNA was obtained from archived neonatal umbilical cord blood. Associations were assessed using sex-stratified Mantel–Haenszel analyses and multiple logistic regression. In sex-stratified Mantel–Haenszel analyses, rs227731 AA was associated with lower odds of OFCs (OR = 0.59; 95% CI: 0.39–0.88; reported p = 0.005), and CC with higher odds (OR = 1.56; 95% CI: 1.02–2.39; reported p = 0.020). These findings were nominal. In the multiple logistic regression models for OFCs overall, neither genotype reached nominal significance. The rs227731 CC genotype showed a nominal association with unilateral cleft lip and palate in the regression analyses. The study identified nominally statistically significant associations between rs227731 at the NOG -associated locus and non-syndromic orofacial clefts in the Polish cohort, with findings differing by analytical model and cleft phenotype. However, these associations did not remain statistically significant after the conservative Bonferroni correction for the 210 association tests documented in the full statistical report. The findings therefore suggest a potential association that requires confirmation in an independent cohort and do not establish clinical predictive utility.